Heterosis and differential gene expression in hybrids and parents in Bombyx mori by
digital gene expression profiling
Hua Wang1,3, , Yan Fang1,4, , Lipeng Wang1, Wenjuan Zhu1, Haipeng Ji1, Haiying
Wang1, Shiqing Xu1,2, Yanghu Sima1,2,*
1
Department of Applied Biology, School of Biology and Basic Medical Sciences,
Medical College of Soochow University, Suzhou 215123, China.
2
National Engineering Laboratory for Modern Silk, Soochow University, Suzhou
215123, China.
3
Department of Cell Biology and Genetics, College of Life Sciences, Nankai
University, Tianjin 300071, China.
4
Department of Immunology, Nankai University School of Medicine, Tianjin
300071, China.
* Correspondence: Yanghu Sima, Department of Applied Biology, School of
Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou
215123, China.
Tel.: +86 0512 65880255; fax: +86 0512 65880255;
E-mail: simyh@suda.edu.cn

These authors contributed equally to this work.
Supplementary Information
Figure S1 Heterosis of silkworms for economical characteristics. (A) Larva-pupa
survival rate (%), (B) Pupa unified vital rate (%). (C) Dead worm cocoon rate (%). (D)
Egg quantities of single moths (egg grains). (E) Cocoon shell weight (g, CSW). (F)
Whole cocoon weight (g, WCW). (G) Pupal weight (g, PW). (H) Cocoon shell percentage
(%, CSP).(I) Length of fiber (m, LF). (J) Diameter of silk fiber (dtex, DSF). C-F1
indicates the crosses F1 offpsring and A-F1 means the reciprocal cross F1 offpsring. (K)
Heterosis of silkworms. The error bars indicate standard deviation. * indicates p < 0.05
using paired two-tailed T-test.
Figure S2 Distribution of total tag types for eight DGE libraries. Raw sequences had
3'-adaptor fragments, a few low-quality sequences and several types of impurities. Raw
sequences were transformed into clean tags after data processing.
Figure S3 Distribution of clean tags. Heterogeneity and redundancy were two
significant characteristics of mRNA expression. A small percentageof categories of
mRNA had very high abundance, while the majority had a low level of expression. The
distribution of clean tag expression was used to evaluate the normality of the data.
Figure S4 Saturation analysis of sequencing. Saturation analysis was performed to
check if the number of detected genes increased as sequencing amount (total tag number)
increased.
Figure S5 Distribution of total clean tags. The numbers in square brackets indicate the
range of copy numbers of each tag category. The data in parentheses indicate the
percentage of corresponding tags among the total clean tags.
Figure S6 Mapping of total clean tags. All clean tags were mapped to reference
sequences and only allowed no more than 1 nt mismatch.
Table S1 Classification Standard of differential gene expression patterns in this
study
75xin×”7532” OR
“7532”×75xin Group
F1 Compared with
F1 Compared with
Female parent(P1)
Male parent(P2)
=log2（F1-TPM/P1-TPM） =log2（F1-TPM/P2-TPM）
Fold
No Difference, ND
Over Parents, OPS
Under Parents, UPS
Under Female, UF
Under Male, UM
Over Female, OF
Over Male, OM
Between Female and Male, FAM
Between Male and Female, MAF
-2<Fold<2
2≤Fold
Fold≤-2
Fold≤-2
-2<Fold<2
2≤Fold
-2<Fold<2
Fold≤-2
2≤Fold
Table S2 Primers for qPCR
Gene
Sense
-2<Fold<2
2≤Fold
Fold≤-2
-2<Fold<2
Fold≤-2
-2<Fold<2
2≤Fold
2≤Fold
Fold≤-2
Anti-sense
Product
BGIBMGA010975
CCAATGGAACAGTGGGAGC
GTCATCATCAGGCGTTACAG
94
BGIBMGA012524
GCCTCCCTATCAAAAGCAAC
CCCTCACAGAACCCTGGCTGAG
144
BGIBMGA013545
GGCTACGACACTTGAGGAATCTG
TGAGGTGGCTTGCCTGATG
125
BGIBMGA010172
CTCCTTCTCAACACAGCCCTAT
GCAGTAACATTTCCTCCACTTCTTC
165
BGIBMGA014427
TCTTGCCGCTATGGTGATTACT
GCGTGCGTCCTTGAGAGTTC
128
BGIBMGA007230
TACCGATTCCCCTACCTC
CTGCTTTCTCCGCCTCCA
102
BGIBMGA003210
CGAGCACTCAGCGGGACA
TACACCCACTATCTAACAACCA
140
BGIBMGA010732
ACCACTTCAACCAGCCCG
GACACTGTAACGCCGACC
126
BGIBMGA010722
ATCGGCTGGGTCGGAAAC
GCTGGCGAGGCACTTGGT
127
BGIBMGA010275
GGAAACTGAAACCGAGACT
TCAACAAGCCATCAAACC
311
BGIBMGA012774
CCGCAGAAACTAAAACACCCTAAC
GCCGTCTCTCTTTGAACCACAT
146
BGIBMGA011868
TCTGGAGTCTGCCTTTAC
GCGTGCTCTGTCTGTGTT
132
BGIBMGA000066
GCATCAATCGGATCGCTATG
GGACCTTACGGAATCCATTTG
147
Table S3 P value of correlation analysis
P value
UM
OM
UF
OPS
OF
UPS
MAF
FAM
Pupae weight
0.068967
0.167353
0.477
0.174811
0.474599
0.46791
0.019403
3.39E-05
Cocoon shell weight
0.30629
0.143714
0.027
0.137304
0.032773
0.025539
0.000416
6.65E-07
Whole cocoon weight
7.52E-06
2.28E-05
2E-04
2.42E-05
0.00013
0.00017
0.010972
0.221616
Cocoon shell percentage
2.27E-06
6.87E-06
5E-05
7.3E-06
3.93E-05
5.15E-05
0.00343
0.443258
Length of fiber
1.71E-07
5.17E-07
4E-06
5.48E-07
2.95E-06
3.87E-06
0.000264
0.118082
Diameter of silk fiber
4.33E-07
1.31E-06
9E-06
1.39E-06
7.49E-06
9.83E-06
0.000666
0.233495